Structure of PDB 5ybi Chain B

Receptor sequence

>5ybiB (length=345) Species: 623 (Shigella flexneri)

HMHTQVGRGLLGAVVNPLGEVTDKFAVTDNSEILYRPVDNAPPLYSERAA
IEKPFLTGIKVIDSLLTCGEGQRMGIFASAGCGKTFLMNMLIEHSGADIY
VIGLIGERGREVTETVDYLKNSEKKSRCVLVYATSDYSSVDRCNAAYIAT
AIAEFFRTEGHKVALFIDSLTRYARALRDVALAAGESPARRGYPVSVFDS
LPRLLERPGKLKAGGSITAFYTVLLEDDDFADPLAEEVRSILDGHIYLSR
NLAQKGQFPAIDSLKSISRVFTQVVDEKHRIMAAAFRELLSEIEELRTII
DKPGENASQDKIYNKISVVESFLKQDYRLGFTYEQTMELIGETIR

3D structure

• PDB: 5ybi Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri.
• Chain: B
• Resolution: 2.268 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K165 E188 R189 R350
• Catalytic site (residue number reindexed from 1): K84 E107 R108 R269
• Enzyme Commision number: 7.4.2.8: protein-secreting ATPase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	B	I186 S250 R253	I105 S169 R172
BS02	MG	B	G177 A178 Y181 K205	G96 A97 Y100 K124
BS03	MG	B	I342 S344	I261 S263
BS04	MG	B	M169 D249	M88 D168
BS05	MG	B	H4 M5 D120	H1 M2 D39
BS06	MG	B	R117 P118 N121	R36 P37 N40
BS07	MG	B	E195 T196	E114 T115
BS08	MG	B	T85 L99 G100	T4 L18 G19
BS09	MG	B	Q86 G100	Q5 G19
BS10	MG	B	E373 K400	E292 K315
BS11	MG	B	F279 E318	F198 E237

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0009058 biosynthetic process
• GO:0030254 protein secretion by the type III secretion system

Cellular Component

• GO:0005737 cytoplasm
• GO:0030257 type III protein secretion system complex

External links

• PDB: RCSB:5ybi, PDBe:5ybi, PDBj:5ybi
• PDBsum: 5ybi
• PubMed: 30013545
• UniProt: P0A1C1|SCTN_SHIFL Type 3 secretion system ATPase (Gene Name=sctN)